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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__message_8c_source.html below:

NCBI C++ ToolKit: src/algo/blast/core/blast_message.c Source File

38

=

"Could not calculate ungapped Karlin-Altschul parameters due " 39 "to an invalid query sequence or its translation. Please verify the " 40 "query sequence(s) and/or filtering options"

;

52 if

( !filename || !(strlen(filename) > 0) ) {

85 if

(blast_msg ==

)

103 int context

,

const char

*message)

107 if

(blast_msg ==

)

111 if

(new_msg ==

)

121 while

(var_msg->

)

123

var_msg = var_msg->

;

125

var_msg->

= new_msg;

129

*blast_msg = new_msg;

138 if

(blast_msg ==

)

141

fprintf(stderr,

"%s"

, blast_msg->

);

163 switch

(error_code) {

166

new_msg->

=

(

"Failed to calculate ideal Karlin-Altschul " 172

new_msg->

=

(

"Composition based statistics or " 173 "Smith-Waterman not supported for your " 179

new_msg->

=

(

"BLAST search interrupted at user's request"

);

204

new_msg->

=

(

"Invalid argument to function"

);

209

new_msg->

=

(

"search cannot proceed due to errors in all " 210 "contexts/frames of query sequences"

);

216

new_msg->

=

(

"The average subject length is too short"

);

222

new_msg->

=

(

"search cannot proceed due to errors " 223 "retrieving sequences from databases"

);

228

new_msg->

=

(

"Database memory map file error"

);

233

new_msg->

=

(

"Too many open files, please raise the open file limit"

);

246

snprintf(

,

sizeof

(

) - 1,

"Unknown error code %d"

, error_code);

256

(

unsigned int

)

);

264

var->

= new_msg;

Definitions used throughout BLAST.

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

const char * kBlastErrMsg_CantCalculateUngappedKAParams

void Blast_PerrorEx(Blast_Message **msg, Int2 error_code, const char *file_name, int lineno, int context)

Extended version of Blast_Perror which includes parameters for the file name and line number where th...

void Blast_Perror(Blast_Message **msg, Int2 error_code, int context)

Analogous to perror.

Int2 Blast_MessagePost(Blast_Message *blast_msg)

Print a message with ErrPostEx.

SMessageOrigin * SMessageOriginFree(SMessageOrigin *msgo)

Deallocate a SMessageOrigin structure.

Int2 Blast_MessageWrite(Blast_Message **blast_msg, EBlastSeverity severity, int context, const char *message)

Writes a message to a structure.

const int kBlastMessageNoContext

Declared in blast_message.h as extern const.

SMessageOrigin * SMessageOriginNew(const char *filename, unsigned int lineno)

Allocate a new SMessageOrigin structure.

Blast_Message * Blast_MessageFree(Blast_Message *blast_msg)

Deallocates message memory.

Structures for BLAST messages.

EBlastSeverity

Blast error message severities .

#define BLASTERR_INTERRUPTED

BLAST search was interrupted via a user-provided callback.

#define BLASTERR_IDEALSTATPARAMCALC

Could not compute the ideal Karlin-Altschul parameters.

#define BLASTERR_SUBJECT_LENGTH_INVALID

Subject seqs min avg length error.

#define BLASTERR_NOVALIDKARLINALTSCHUL

Could not calculate Karlin-Altschul statistics for any context.

#define BLASTERR_INVALIDQUERIES

All queries/contexts are determined invalid in the setup code.

#define BLASTERR_SEQSRC

Blast seqsrc returns BLAST_SEQSRC_ERROR.

#define BLASTERR_DB_MEMORY_MAP

Database file error.

#define BLASTERR_DB_TOO_MANY_OPEN_FILES

#define BLASTERR_REDOALIGNMENTCORE_NOTSUPPORTED

Composition based statistics/Smith-Waterman not supported for a program type.

#define BLASTERR_MEMORY

System error: out of memory condition.

#define BLASTERR_INVALIDPARAM

Invalid parameter: possible programmer error or pre-condition not met.

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

int16_t Int2

2-byte (16-bit) signed integer

#define ASSERT

macro for assert.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Structure to hold the a message from the core of the BLAST engine.

int context

Context, allows us to print message for query number.

EBlastSeverity severity

severity code

SMessageOrigin * origin

Optional: origin of the message.

char * message

User message to be saved.

struct Blast_Message * next

next message in this list

Structure to enclose the origin of an error message or warning.

int lineno

Line number in the file above.

char * filename

Name of the file.

static CS_CONTEXT * context

voidp calloc(uInt items, uInt size)

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